diff --git a/stdpopsim/catalog/MusMus/__init__.py b/stdpopsim/catalog/MusMus/__init__.py index 844fb86de..e813ba667 100644 --- a/stdpopsim/catalog/MusMus/__init__.py +++ b/stdpopsim/catalog/MusMus/__init__.py @@ -3,3 +3,4 @@ """ from . import species # noqa: F401 from . import demographic_models # noqa: F401 +from . import genetic_maps # noqa: F401 diff --git a/stdpopsim/catalog/MusMus/genetic_maps.py b/stdpopsim/catalog/MusMus/genetic_maps.py new file mode 100644 index 000000000..e106711af --- /dev/null +++ b/stdpopsim/catalog/MusMus/genetic_maps.py @@ -0,0 +1,31 @@ +import stdpopsim + +_species = stdpopsim.get_species("MusMus") + +_genetic_map_citation = stdpopsim.Citation( + doi="https://doi.org/10.1534/genetics.109.105486", + author="Cox et al.", + year=2009, + reasons={stdpopsim.CiteReason.GEN_MAP}, +) + +_gm = stdpopsim.GeneticMap( + species=_species, + id="Cox_etal_2009_v3_GRCm39", # ID for genetic map, see naming conventions + description="Revised Cox genetic map, for mouse genome build 39 coordinates", + long_description=""" + This map results from the Cox et al. (2009) genetic map which has been + lifted over to the GRCm39 genome which was released in 2020. As described in + the abstract of Cox et al. (2009), the genetic map resulted from a large + heterogeneous mouse population and incorporates 10,195 SNPs using a set + of 47 families comprising 3546 meioses. The methods by which this original + map was lifted to the GRCm39 genome are described on a github repo: + https://github.com/kbroman/CoxMapV3 + """, + url=("https://stdpopsim.s3-us-west-2.amazonaws.com/genetic_maps/dir/cox.tar.gz"), + sha256="d589a7adf334f31343aff722aeebe96b1663cab573856d80a883f07bd3cb9b11", + file_pattern="Cox_etal_2009_v3_GRCm39_{id}.txt", + citations=[_genetic_map_citation], +) + +_species.add_genetic_map(_gm)